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First, define a custom output variable at the system timestep which is summed (not averaged). Let's say the value you are reporting is "MyEMSOutput".

EnergyManagementSystem:OutputVariable ,
MyEMSOutputVariable[units], !- Name
MyEMSOutput , !- EMS Variable Name
Summed , !- Type of Data in Variable
SystemTimeStep; !- Update Frequency

Then, report it at the zone timestep frequency. EnergyPlus will accumulate (sum) the variable at the end of every system timestep and then report it at the end of every zone timestep.

Output:Variable,
*, !- Key Value
MyEMSOutputVariable, !- Variable Name
Timestep; !- Reporting Frequency